Aperio scanscope at2

Placentas were fixed with 4% PFA, dehydrated in ethanol, and embedded in paraffin. Sections (5 µm thick) were cut using a microtome and mounted on either Superfrost Plus Slides (R. Langenbrinck, Emmendingen, Germany) for immunohistochemistry or standard slides (Engelbrecht Medizin- und Labortechnik GmbH, Edermünde, Germany) for Masson–Goldner trichrome (MGT), periodic acid Schiff (PAS), and placental alkaline phosphatase (PLAP) staining.
Digitalization of the stained slides was conducted by the West German Biobank, University Hospital Essen. The slides were scanned with an Aperio ScanScope AT2 (Leica, Wetzlar, Germany) at 40× magnification in transmission mode. Digital images were converted into TIFF files using Image Scope (Version 12.3.3.5048, Leica) and analyzed with ImageJ/FIJI (Version 1.53t) [47 (link)]. Morphometric analyses were performed on placenta sections in the region of the umbilical cord.

Images of GFAP and D2R immunofluorescence were captured with a confocal Leica SPE microscope. For the mouse tissue, five z-stack images (total thickness 15 μm) were taken per region of interest (CA1, CA3 and DG region of the hippocampus and the striatum) at 40x magnification. For the human post-mortem tissue, 10 z-stack images (total thickness 5 μm) were acquired at 40x magnification in the CA1 region of the hippocampus. Post-mortem tissue sections which were stained for GFAP using immunohistochemistry were sent to the Histopathology/HIS facility at the Cancer Research UK Cambridge Institute and were imaged using an Aperio Scanscope AT2 (Leica Biosystems) at a 20x magnification, with a resolution of 0.503 µm per pixel.

Next, the remaining half-sliced lumpectomy specimen was further processed by the Department of Pathology, where sagittal slicing and gross sectioning of the lumpectomy specimen continued. The measured tissue slice, the surface of which the optical tissue measurements were performed, was then placed in a megacasette (Figure 6g). According to the standard protocol, a microscopic H&E section was created and digitalized with Aperio^® ScanScope AT2 (Leica Biosystems, Wetzlar, Germany) (Figure 6h). All histology images were uploaded to Slide Score (web viewer for high-resolution scans of microscopic histopathology slides). Here, for each microscopic H&E image, invasive carcinoma, ductal carcinoma in situ (DCIS), and connective and fat tissue were annotated by a pathologist and considered as the ground truth (Figure 6i). After finalizing the complete histopathology processing of the lumpectomy specimen, two different microscopic images were generated: a histology image of the measured breast specimen ( $H_O$ ) and an annotated histology image of the measured breast specimen ( $H_A$ ).